Geometry between Cylinders and Cuboids
Match face-count and keep the flow of the edges

Assuming that you would like to create a sort of "basemesh" to start to work with, I suggest you should:


keep a the polycount low, it will be faster to make adjustement
keep a quad oriented topology, it increase the edgeflow redabilty and helps to keep the model "clean"
keep a quad oriented topology, because you said you are going to subsurf the model, and quads give best results
work with the subsurf modifier so you can easily check if everithing is going the way you are expecting and to place correct additional edge loops


Here's a possible topology fort this particular case with the previous characteristics:



Notice how three of the 8 faces that makes the cylinder are "bridged" to other 3 faces of the the other mesh. This allow a good junction between the pieces like they were welded that will give good results once the mesh is being subsurfed.



Here's the final result with subsurf in action: